PHI: Portal for Health Informatics

Molecular Interactions

Molecular Interactions are crucial for a function of biological system, there are wide range of interactions. Our group mainly focussed on prediction of molecules interacting residues in a protein. Broadly, these servers predict; i) glycosylation sites, ii) small molecules (e.g., ATP, GTP) interacting sites, iii)nucleotide binding sites and iv) protein-protein interaction.

Predicting Interaction between biomolecules (Raghava's Group)

1. ADPint:Predicion of ADP interacting residue.
2. ATPint: Identification of ATP binding sites in ATP-binding proteins.
3. CRIP: Computational Resources for molecular Interaction Prediction
4. DNAint: Prediction of DNA Interacting Residues.
5. GlycoEP: Prediction of C-, N- and O-glycosylation site in eukaryotic proteins. 
6. GlycoPP: Prediction of potential N-and O-glycosites in prokaryotic proteins.
7. GTPbinder: Identification of GTP binding residue in protein sequences. 
8. HIVint: Prediction of protein-protein interaction between HIV and Human proteins.
9. LPIcom: Analysis and prediction of ligand protein interaction.
10. NADbinder: Prediction of NAD interacting residues in proteins.
11. NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence
12. PAAINT: A webservice for predicting residue-residue contacts in proteins.
13. PPDBench:  Benchmarking of docking software on protein-peptide complexes.
14. Pprint:  A  web-server for predicting RNA-binding residues of a protein.
15. PreMieR:  A webserver for the prediction of Mannose Interacting residue.
16. ProPrInt: A web-server predicts physical or functional interactions between protein molecules.
17. RISICbinder: Prediction of guide strand of microRNAs from its sequence and secondary structure.
18. RNAint: Identification of RNA interacting residues in a protein.
19. RNApin: Prediction of Protein Interacting Nucleotides (PINs) in RNA sequences.
20. RNApred: A webserver for the prediction of RNA binding proteins.
21. RRCpred: A Webserver for predicting residue-residue contact.
22. SAMbinder: Web Server for Predicting S-Adenosyl-L-Methionine Binding Residues of a Protein From Its Amino Acid Sequence
23. VitaPred: A webserver for predicting the vitamin interacting residue.

External Links to web servers developed/maintained by other groups

This section provides URL/links to important websites developed and maintained by other researchers. It exclude servers by Raghava's group, which is given in above section. 

1. ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein:ligand complex.
2. COILCHECK: an interactive server for the analysis of interface regions in coiled coils.
3. DenHunt : A Comprehensive Database of the Intricate Network of Dengue-Human Interactions.
4. DRGAS: a database of functional genetic variants and their phosphorylation states in human DNA repair systems.
5. ECMIS: computational approach for the identification of hotspots at protein:protein interfaces.
6. EnPPIpred: Prediction of Intra-Species Protein-Protein Interactions in Enteropathogens Facilitating Systems Biology Study.
7. HADDOCK: Describes the modelling and interaction of bio-molecular complexes such as protein-protein, protein-DNA
8. HORI: a web server to compute Higher Order Residue Interactions in protein structures.
9. Hu-Vir: Molecular principles of human virus protein-protein interactions.
10. MolSurfer:  A Macromolecular Interface Navigator.
11. PathBLAST: "Search protein-protein interaction network of any selected organism and extracts all interaction pathways "
12. PLIC: protein:ligand interaction clusters.
13. PPIMpred: A web server for high-throughput screening of small molecules targeting protein-protein interaction.
14. PRDBv2: A non-redundant protein-RNA docking benchmark version 2.0.
15. SigMol: Repertoire of quorum sensing signaling molecules in prokaryotes.
16. SPEER-SERVER: a web server for prediction of protein specificity determining sites.